stat_unique

Remove duplicates and then convert them with ggplotly.

p <-    
 ggplot(mtcars, aes(vs, am)) +
  geom_point(alpha = 0.1)

plotly::ggplotly(p)

p <-    
 ggplot(mtcars, aes(vs, am)) +
  geom_point(alpha = 0.1, stat = "unique")

plotly::ggplotly(p)